LineagePulse

Lineage 1

Percentage of genes called significant as we change q-value threshold

## 62.2% of the genes are called significant when we require the adjusted p-value to be smaller than 0.01

Heatmap of significant genes

Visualization of 9 most significant genes

Visualization of 9 least significant genes

Lineage 2

Percentage of genes called significant as we change q-value threshold

## 76.16% of the genes are called significant when we require the adjusted p-value to be smaller than 0.01

Heatmap of significant genes

Visualization of 9 most significant genes

Visualization of 9 least significant genes

Observation

• Most of the genes (~70%) are called significant under a commonly used significant level 0.01.
• LineagePulse works well in detecting time-varying genes. However, it is very sensitive to outliers: several of the most significant genes are detected simply due to outliers (?) as shown in the heatmap.